How to Read a Scientific Paper (About That Researcher With a Nematode in His Mouth)

Too often we open a journal, scan the title of a scientific paper – for instance, “Gongylonema pulchrum in a Resident of Williamsburg, Virginia, Verified by Genetic Analysis” – and dismiss it. We think “Yeah, yeah, infection in a small Virginia town” – and turn the page.

Later we may regret that.

Later we may realize that if we’d actually read the paper– or at least read between the lines – we would have discovered a story worth our time. Perhaps the story of a biologist who pulled a nematode out of his cheek with a pair of forceps. Really good forceps, according to the paper: “#5 super fine tip, Roboz Surgical Instrument Co. Inc.” forceps.

But I’m getting ahead of myself. The forceps come later in the story.

Let’s rewind to September 2012. It was about then- according to this recently published report (paywall) in The American Journal of Tropical Medicine – that an “otherwise healthy, 36-year-old man” felt a rough patch in his mouth, a scaly little area in his right cheek. It didn’t hurt. But then it didn’t stay there either. He started testing for it with his tongue. It traveled. It moved to the back of his mouth, then forward, coiled backwards again. In the language of science: “These rough patches would appear and disappear on a daily basis, giving the patient the indirect sense that there was an organism moving within the oral cavity.”

Or in the English language: “Yuck.”

In the interests of transparency, the science journalist confesses that “yuck” was her reaction. Not so for the scientist, apparently. As the paper also tells us, the patient was “coincidentally trained as an invertebrate biologist.” A little journalistic investigation finds that this is scientific code for “Jonathan D. Allen,” who is one of the coauthors of the paper.

Further investigation leads to a phone call with Prof. Allen. He works at the College of William and Mary’s biology department. He’s fascinated by crawly little lifeforms. “Yuck” never crossed his mind.

“Wow, this is really interesting,” thought Allen. And then 1) I hope it’s not fatal and 2) I hope it’s publishable. Although the journalist may have listed those in the wrong order. After all, Allen did email his colleagues with the subject line: “A paper in my mouth.”

In mid-December, as the paper tells us: “The patient was able to visualize the rough patch in the mucosa of his lower lip after migration of the worm towards the opening of the mouth.” In other words, in the midst of giving a final exam, Allen realized that the creature had journeyed to the front of his mouth. As soon as the exam was over, he rushed to the men’s room, pulled down his lip, and saw the coiling structure of a tiny worm-like creature just under the inner skin.

Was he thrilled? He took pictures (which you will find in the paper). He pulled down his lip to show his colleagues (those who would look). He took more pictures. He used the images to do internet research (yes, Google) and made a tentative identification of the creature in his mouth as a parasitic nematode best known for inhabiting the mouths of livestock.

And then he called his doctor. Who referred him to an oral surgeon. Who didn’t believe him.

Really.

Referring back to the paper: “Upon presenting the oral surgeon with photographic evidence (Figure 1A and B) and a detailed description and preliminary diagnosis of gongylonemiasis, the surgeon disputed the patient’s self-diagnosis, claiming this was simply normal discoloration of the skin.”

Referring back to my notes: “My jaw just dropped,” Allen said. But he couldn’t change the surgeon’s mind. “I said, ‘Look, I study these things for a living’. And he said, ‘Well, I look in people’s mouths every day.” The scientist and surgeon did not part on a happy note. “I paid my co-pay and left. It was totally depressing.”

And he stayed depressed – “I’d lost faith in the medical profession” – until he woke up about 3 a.m. the following morning. The spot had moved toward the front of his mouth again. He realized could remove the worm himself.

Of course, he needed help. No surgeon can work alone. He woke up his wife (Margaret Pizer, a communications specialist for Virginia Sea Grant) so that she could shine a flashlight in his mouth. With those #5 super fine tip Roboz Surgical Instrument forceps, he gently scraped the lining of his mouth until he was able to pull out the nematode. It came coiling out, a little less than an inch in length. It was not a happy parasite. “It was writhing.”

Referring to the paper: “The living and highly active parasite was transported to the patient’s research laboratory at the College of William and Mary.”

Referring to my notes: Still in his pajamas, Allen hurried to campus. He had the live parasite in a vial, floating in his spit. When he got to the lab, he took further measurements and then dropped it into a container with an ethanol solution to preserve it.

And referring one more time to the paper (the one you should have stopped and read): “The long transparent worm was readily identified as a nematode belonging to the genus Gongylonema.”

Allen discovered that he was the 13th known human in the United States to be infected by the nematode. He’s still trying figure out how he acquired his companion – he speculates that the worm could have been in his wellwater or in something he ate, possibly in a box of raisins. Globally, there’s no clear pattern to such cases except that they are rare. Scientists have identified some 50 or so cases of human infection; the first was reported in 1996 in Japan.

So Allen wanted to be sure that this was indeed the parasite that he’d extracted from his cheek. A colleague from Eastern Virginia Medical School, who specialized in genetic analysis came forward to help him make a more detailed identification. Aurora Esquela-Kerscher fell completely into the spirit of the research. No Gongylonema for her laboratory. She suggested they call the nematode “Buddy.” As in: Let’s use PCR (polymerase chain reaction) to amplify Buddy’s DNA, detail the exact genetic sequence, and verify his identification. Which is what they did; this was, in fact, the first paper to do genetic analysis of this over-friendly little nematode.

“It’s the only paper I’ve ever published in a medical journal,” Allen says. “It’s a fun story to tell and it grosses my students out. But also I’m at a college where we train a lot of pre-med students. We always debate what they need to know, how to give them the ability to think critically and to see things that are not normal.”

In other words, a good scientific paper will remind you that your definition of “normal” is way too narrow. Okay, now you can turn the page.

Image: Buddy, the nematode, suspended in ethanol solution, courtesy of Jonathan D. Allen, Department of Biology, College of William and Mary.